[chimerax-users] Open AmiraMesh 3.0 in ChimeraX

[Roden Deng Luo]

Hi Tom,

Thanks very much! After changing the first line to 2.1, it tells me "Did
not find "define Lattice" mesh size line". So I guess there are some
"fundamental" changes.

The only .am file I have now is quite large in terms of debugging (64MB). I
found two examples by googling "AmiraMesh BINARY-LITTLE-ENDIAN "3.0"". They
give me "Did not find "Lattice { float ... }" line" after fooling ChimeraX.
In case I get a smaller one or I got to know the way to crop only a small
section and export a smaller one. I will let you know. I will also go
through "Report a Bug".

https://edmond.mpdl.mpg.de/imeji/file/60/17/dc/32-bf46-4e34-b9ba-f02d2fe070b4/0/original/ae8b3e16a7a0f881f66b804ceac50b97.am?filename=190522a_STACK.labels.am
https://edmond.mpdl.mpg.de/imeji/exportServlet?format=file&id=http://edmond.mpdl.mpg.de/imeji/item/IoNX5MO0lyzezIwX

Thanks,
Roden


On Mon, Oct 25, 2021 at 8:37 PM Tom Goddard <goddard at sonic.net> wrote:

> Hi Roden,
>
> The ChimeraX reader is for AmiraMesh format 2.1 and you are trying to read
> a version 3.0 file.  I don't know if those are compatible.  You can test by
> making ChimeraX not check the Amira file version by editing the following
> file  (location for Mac, ChimeraX 1.3 daily build shown)
>
>
> ChimeraX.app/Contents/lib/python3.9/site-packages/chimerax/map_data/amira/amira_format.py
>
> changing these lines
>
>     if not (line.startswith(b'# AmiraMesh BINARY-LITTLE-ENDIAN 2.1') or
>             line.startswith(b'# Avizo BINARY-LITTLE-ENDIAN 2.1')):
>       raise SyntaxError('First line of AmiraMesh file must start with '
>                         '"# AmiraMesh BINARY-LITTLE-ENDIAN 2.1", '
>                         'instead got "%s"' % line[:256])
>
> to
>
> #    if not (line.startswith(b'# AmiraMesh BINARY-LITTLE-ENDIAN 2.1') or
> #            line.startswith(b'# Avizo BINARY-LITTLE-ENDIAN 2.1')):
> #      raise SyntaxError('First line of AmiraMesh file must start with '
> #                        '"# AmiraMesh BINARY-LITTLE-ENDIAN 2.1", '
> #                        'instead got "%s"' % line[:256])
>
> so the version test will not be done.
>
>   Or you could use ChimeraX menu Help / Report a Bug... and attach a
> modest size Amira 3.0 file and I can try it.
>
>   Or you could make a copy of your Amira file and edit the first line so
> instead of saying it is version 3.0 it says it is version 2.1.
>
> Tom
>
>
> On Oct 23, 2021, at 8:12 AM, Roden Deng Luo via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> Dear ChimeraX Users,
>
> I have an AmiraMesh .am file exported from Amira 3D 2021.1 (Build date:
> 2021-06-21 13:21:22, SHA id: 213bd1......13c73e). When I load it into
> ChimeraX 1.2.5 or ChimeraX 1.3.dev202110231141, ChimeraX tells me the
> following error.
>
> First line of AmiraMesh file must start with "# AmiraMesh
> BINARY-LITTLE-ENDIAN 2.1", instead got "b'# AmiraMesh BINARY-LITTLE-ENDIAN
> 3.0\n'"
>
> Googling "AmiraMesh site:
> https://www.rbvi.ucsf.edu/pipermail/chimerax-users
> <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/pipermail/chimerax-users__;!!Nmw4Hv0!gswyBcLggCUszrrkzuG1NAh0dA6mXVnN-mOrDaZJKGhoRMCix2NZTs_HZ5w3Eiak_ks$>"
> shows no result. Can anyone kindly help here?
>
> Many thanks,
> Roden
>
>
>
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